diff illuminapairedend.xml.orig @ 4:d0f6ac976373 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/illuminapairedend.xml.orig	Wed Sep 01 07:49:38 2021 +0000
@@ -0,0 +1,169 @@
+<<<<<<< HEAD
+<tool id="obi_illumina_pairend" name="Illuminapairedend" version="@TOOL_VERSION@" profile="@PROFILE@">
+    <description>Construct consensus reads from Illumina pair-end reads</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command>
+        <![CDATA[
+        #if $inputfastq3p.ext.endswith(".gz")
+            gunzip -c '$inputfastq3p' > fastq3p.fastq &&
+            gunzip -c '$inputfastq5p' > fastq5p.fastq &&
+        #else
+            ln -s '$inputfastq3p' fastq3p.fastq &&
+            ln -s '$inputfastq5p' fastq5p.fastq &&
+        #end if
+
+        illuminapairedend
+        ##--index-file=
+        #if $inputfastq3p.ext.startswith("fastqsolexa")
+            ##input file is in fastq nucleic format produced by solexa sequencer
+            --solexa
+        #else if $inputfastq3p.ext.startswith("fastqillumina")
+            ##input file is in fastq nucleic format produced by solexa sequencer
+            --illumina
+        #else
+            ## input file is in sanger fastq nucleic format (standard fastq)
+            --sanger
+        #end if
+        --without-progress-bar
+        --score-min='$score'
+        -r fastq3p.fastq 
+        fastq5p.fastq
+        #if $inputfastq3p.ext.endswith(".gz")
+            | gzip -c 
+        #end if
+        > '$output'
+        ]]>
+    </command>
+    <inputs>
+        <param name="inputfastq3p" type="data" format="fastq,fastq.gz" label="Read from file" help="file of 3p (1:) Illumina pair-end reads to assemble in sanger fastq nucleic format (standard fastq)" />
+        <param name="inputfastq5p" type="data" format="fastq,fastq.gz" label="Read from file" help="file of 5p (2:) Illumina pair-end reads to assemble in sanger fastq nucleic format (standard fastq)" />
+        <param name="score" type="float" value="40.0" label="minimum score for keeping aligment"/>
+    </inputs>
+    <outputs>
+        <data name="output" format_source="inputfastq3p" label="${tool.name} on ${on_string}: assembly results" />
+    </outputs>
+
+    <tests>
+       <test>
+           <param name="inputfastq3p" value="wolf_small.F.fastq" ftype="fastqsanger" />
+           <param name="inputfastq5p" value="wolf_small.R.fastq" ftype="fastqsanger" />
+           <param name="score" value="40.0" />
+           <output name="output" file="illuminapairedend.output.fastq" ftype="fastqsanger" />
+       </test>
+       <test>
+           <param name="inputfastq3p" value="wolf_small.F.fastq.gz" ftype="fastqsanger.gz" />
+           <param name="inputfastq5p" value="wolf_small.R.fastq.gz" ftype="fastqsanger.gz" />
+           <param name="score" value="40.0" />
+           <output name="output" file="illuminapairedend.output.fastq.gz" ftype="fastqsanger.gz" decompress="true"/>
+       </test>
+   </tests>
+
+    <help><![CDATA[
+
+.. class:: warning
+
+**Warning:**
+Sequence records corresponding to the same read pair must be in the same order in the two files
+
+--------
+
+.. class:: infomark
+
+**What it does**
+
+illuminapairedend aims at aligning the two reads of a pair-end library sequenced using an Illumina platform :
+
+\* If the two reads overlap, it returns the consensus sequence together with its quality
+\* Otherwise, it concatenates sequence merging the forward read and the reversed-complemented reverse read.
+
+The program uses as input one or two fastq sequences reads files.
+
+\* If two files are used one of them must be specified using the -r option. Sequence records corresponding to the  same read pair must be in the same order in the two files.
+\* If just one file is provided, sequence records are supposed to be all of the same length. The first half of th  e sequence is used as forward read, the second half is used as the reverse read.
+
+illuminapairedend align the forward sequence record with the reverse complement of the reverse sequence record. The alignment algorithm takes into account the base qualities.
+
+@OBITOOLS_LINK@
+
+]]>
+    </help>
+    <expand macro="citation" />
+
+</tool>
+=======
+<tool id="obi_illumina_pairend" name="Illuminapairedend - Assembling pair-end reads" version="@TOOL_VERSION@">
+    <description>Construct consensus reads from Illumina pair-end reads</description>
+    <expand macro="bio_tools"/>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command>
+
+        <![CDATA[
+        illuminapairedend
+
+        --score-min='$score'
+        -r '$inputfastq3p'
+        '$inputfastq5p' > '$output'
+
+        ]]>
+
+    </command>
+
+    <inputs>
+        <param name="inputfastq3p" type="data" format="fastq" label="Read from file" help="file of 3p (1:) Illumina pair-end reads to assemble in sanger fastq nucleic format (standard fastq)" />
+        <param name="inputfastq5p" type="data" format="fastq" label="Read from file" help="file of 5p (2:) Illumina pair-end reads to assemble in sanger fastq nucleic format (standard fastq)" />
+        <param name="score" type="float" value="40.0" label="minimum score for keeping aligment"/>
+    </inputs>
+    <outputs>
+        <data format="fastq" name="output" label="${tool.name} on ${on_string}: assembly results" />
+    </outputs>
+
+    <tests>
+       <test>
+           <param name="inputfastq3p" value="wolf_small.F.fastq" />
+           <param name="inputfastq5p" value="wolf_small.R.fastq" />
+           <param name="score" value="40.0" />
+           <output name="output" file="illuminapairedend.output.fastq" ftype="fastq"/>
+       </test>
+   </tests>
+
+    <help><![CDATA[
+
+.. class:: warning
+
+**Warning:**
+Sequence records corresponding to the same read pair must be in the same order in the two files
+
+--------
+
+.. class:: infomark
+
+**What it does**
+
+illuminapairedend aims at aligning the two reads of a pair-end library sequenced using an Illumina platform :
+
+\* If the two reads overlap, it returns the consensus sequence together with its quality
+\* Otherwise, it concatenates sequence merging the forward read and the reversed-complemented reverse read.
+
+The program uses as input one or two fastq sequences reads files.
+
+\* If two files are used one of them must be specified using the -r option. Sequence records corresponding to the  same read pair must be in the same order in the two files.
+\* If just one file is provided, sequence records are supposed to be all of the same length. The first half of th  e sequence is used as forward read, the second half is used as the reverse read.
+
+illuminapairedend align the forward sequence record with the reverse complement of the reverse sequence record. The alignment algorithm takes into account the base qualities.
+
+@OBITOOLS_LINK@
+
+]]>
+    </help>
+    <expand macro="citation" />
+
+</tool>
+>>>>>>> 7abad681f (add tools up until P)